Baking multiple objects with seperate maps at once?
Cycles:

Bake Tool offers support for high to low poly baking of multiple objects. Set it up one object (high poly) and target (low poly) per job. Use multiple jobs for each additional set of objects. Bake Tool can also be used for baking multiple maps in BI. (This is helpful for displacement map baking.)

Meltdown also offers similar support.

As of version 2.78c, Bake Helper does not support high to low poly baking.